Yeah, Reaper is not as well optimized as Protools, or the Quicktime Player. VLC is not really a candidate for comparison, because it's more of a dumb player. The Quicktime Player lets you visually seek in the video, and depending on the codec (single-frame codecs are quickest, delta-frame or Group Of Picture codecs are usually slower) you can locate stuff very quickly.
Reaper is not yet that smart. It will freeze on you if it seemingly cannot decode any frames in time. I'm speculating here as to why it does what it does, but it has to happen somehow. Protools is just lightyears ahead on performance in this area.
I convert a 1024x576 H264 Quicktime to a 512x288 Photojpeg Quicktime(75% quality) of 22 minutes length in about 4 minutes on my i7 920, and it only uses one core.
Converting video is just a reality, and if you don't have a picture department backing you up, taking care of these things, you'll just have to bite the bullet and try to find what works best for your setup.
And continue to pester Cockos to match at least what Protools can do in terms of video seek and playback performance.
Side note. I could play those 512x288 codecs with 10-15% CPU use on an AthlonXP 2500 in PT. The seeking was almost the same speed as it is on the i7 I have now. Yeah, it can be improved.
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